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Background  Georgia, in the Caucasian region, is considered the first domestication centre of grapevine. This country is characterized by high morphological variability of cultivated ( Vitis vinifera  L. subsp.  sativa  (DC.) Hegi) and wild ( Vitis vinifera  L. subsp.  sylvestris  (Gmel.) Hegi) compartments. The main objective of this study was to investigate the level of genetic diversity obtained by the novel custom Vitis18kSNP array, in order to analyse 71 grapevine accessions representative of wild and cultivated Georgian germplasms.    Results  The number of loci successfully amplified was 15,317 out of 18,775 SNP and 79 % of loci resulted polymorphic. Sixty-eight unique profiles were identified, 42 for the  sativa  and 26 for the  sylvestris  compartment. Cluster analysis highlighted two main groups, one for cultivars and another for wild individuals, while a genetic structure according to accession taxonomic status and cultivar geographical origin was revealed by multivariate analysis, differentiating clearly the genotypes into 3 main groups, two groups including cultivars and one for wild individuals, even though a considerable overlapping area was observed.    Conclusions  Pattern of genetic diversity structure presented an additional proof that grapevine domestication events took place in the Caucasian region contributing to the crop evolution. Our results demonstrated a moderate differentiation between  sativa  and  sylvestris  compartments, even though a connection between several samples of both subspecies may be assumed for the occurrence of cross hybridization events among native wild populations and the cultivated accessions. Nevertheless, first degree relationships have not been discovered between wild and cultivated individuals.    Electronic supplementary material  The online version of this article (doi:10.1186/s12870-015-0510-9) contains supplementary material, which is available to authorized users.

Study of genetic variability in Vitis vinifera L. germplasm by high-throughput Vitis18kSNP array: the case of Georgian genetic resources